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Yorodumi- PDB-1g2a: THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g2a | ||||||
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Title | THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ACTINONIN | ||||||
Components | POLYPEPTIDE DEFORMYLASE | ||||||
Keywords | HYDROLASE / actinonin / inhibition / Polypeptide deformylase | ||||||
Function / homology | Function and homology information co-translational protein modification / peptide deformylase / peptide deformylase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Clements, J.M. / Beckett, P. / Brown, A. / Catlin, C. / Lobell, M. / Palan, S. / Thomas, W. / Whittaker, M. / Baker, P.J. / Rodgers, H.F. ...Clements, J.M. / Beckett, P. / Brown, A. / Catlin, C. / Lobell, M. / Palan, S. / Thomas, W. / Whittaker, M. / Baker, P.J. / Rodgers, H.F. / Barynin, V. / Rice, D.W. / Hunter, M.G. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2001 Title: Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor. Authors: Clements, J.M. / Beckett, R.P. / Brown, A. / Catlin, G. / Lobell, M. / Palan, S. / Thomas, W. / Whittaker, M. / Wood, S. / Salama, S. / Baker, P.J. / Rodgers, H.F. / Barynin, V. / Rice, D.W. / Hunter, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g2a.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2a.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 1g2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g2a_validation.pdf.gz | 662.9 KB | Display | wwPDB validaton report |
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Full document | 1g2a_full_validation.pdf.gz | 674.7 KB | Display | |
Data in XML | 1g2a_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1g2a_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2a ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19226.248 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DEF / Plasmid: PET24-PDF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6K3, EC: 3.5.1.31 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.6 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10mg/ml PDF, 20mM actinonin, 50mM HEPES, pH 7.5 + 25-32% PEG 4000, 0.1M sodium citrate, pH 5.6, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP at 290K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 28, 1999 / Details: MSC Yale Mirrors |
Radiation | Monochromator: msc yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→14 Å / Num. all: 62907 / Num. obs: 54729 / % possible obs: 0.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.191 / % possible all: 86.8 |
Reflection | *PLUS % possible obs: 85.9 % |
Reflection shell | *PLUS % possible obs: 86.8 % / Num. unique obs: 3634 / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→14 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.75→14 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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